@nahisaho/satori 0.17.0 → 0.18.0

package/src/.github/skills/scientific-icgc-cancer-data/SKILL.md

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+---
+name: scientific-icgc-cancer-data
+description: |
+  ICGC がんゲノムデータスキル。ICGC ARGO DCC API および
+  レガシー API による国際がんゲノムデータ検索・ドナー/
+  検体/変異解析。直接 API (ToolUniverse 非連携)。
+tu_tools: []
+---
+
+# Scientific ICGC Cancer Data
+
+ICGC (International Cancer Genome Consortium) ARGO DCC API を
+活用した国際がんゲノムデータ検索・変異統計・がん種横断解析
+パイプラインを提供する。
+
+## When to Use
+
+- 国際がんゲノムプロジェクトのデータを検索するとき
+- がん種ごとの体細胞変異プロファイルを調べるとき
+- ドナー・検体・変異の統計情報を取得するとき
+- がんゲノムの変異シグネチャを分析するとき
+- PCAWG (Pan-Cancer Analysis of Whole Genomes) データを活用するとき
+- がん遺伝子変異の国際比較データが必要なとき
+
+---
+
+## Quick Start
+
+## 1. ICGC プロジェクト・ドナー検索
+
+```python
+import requests
+import pandas as pd
+
+ICGC_BASE = "https://dcc.icgc.org/api/v1"
+
+
+def icgc_search_projects(query=None, limit=50):
+    """
+    ICGC — がんゲノムプロジェクト検索。
+
+    Parameters:
+        query: str — 検索キーワード (例: "lung", "BRCA")
+        limit: int — 最大結果数
+    """
+    url = f"{ICGC_BASE}/projects"
+    params = {"size": limit, "from": 1}
+    if query:
+        params["filters"] = (
+            f'{{"project":{{"primarySite":'
+            f'{{"is":["{query}"]}}}}}}'
+        )
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", []):
+        results.append({
+            "project_id": hit.get("id", ""),
+            "project_name": hit.get("name", ""),
+            "primary_site": hit.get("primarySite", ""),
+            "tumour_type": hit.get("tumourType", ""),
+            "tumour_subtype": hit.get("tumourSubtype", ""),
+            "primary_country": "; ".join(
+                hit.get("primaryCountries", [])),
+            "total_donors": hit.get("totalDonorCount", 0),
+            "ssm_count": hit.get("ssmCount", 0),
+        })
+
+    df = pd.DataFrame(results)
+    if not df.empty:
+        df = df.sort_values("total_donors", ascending=False)
+
+    total = data.get("pagination", {}).get("total", 0)
+    print(f"ICGC projects: {len(df)}/{total} "
+          f"(query='{query}')")
+    return df
+
+
+def icgc_search_donors(project_id, limit=100):
+    """
+    ICGC — プロジェクト内ドナー検索。
+
+    Parameters:
+        project_id: str — プロジェクト ID (例: "BRCA-US")
+        limit: int — 最大結果数
+    """
+    url = f"{ICGC_BASE}/donors"
+    params = {
+        "size": limit,
+        "filters": (
+            f'{{"donor":{{"projectId":'
+            f'{{"is":["{project_id}"]}}}}}}'
+        ),
+    }
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", []):
+        results.append({
+            "donor_id": hit.get("id", ""),
+            "project_id": project_id,
+            "primary_site": hit.get("primarySite", ""),
+            "gender": hit.get("gender", ""),
+            "vital_status": hit.get("vitalStatus", ""),
+            "age_at_diagnosis": hit.get("ageAtDiagnosis"),
+            "disease_status": hit.get(
+                "diseaseStatusLastFollowup", ""),
+            "ssm_count": hit.get("ssmCount", 0),
+        })
+
+    df = pd.DataFrame(results)
+    total = data.get("pagination", {}).get("total", 0)
+    print(f"ICGC donors: {len(df)}/{total} "
+          f"(project={project_id})")
+    return df
+```
+
+## 2. 体細胞変異 (SSM) 検索
+
+```python
+def icgc_search_mutations(gene_symbol=None,
+                             project_id=None,
+                             consequence_type=None,
+                             limit=100):
+    """
+    ICGC — 体細胞変異 (Simple Somatic Mutation) 検索。
+
+    Parameters:
+        gene_symbol: str — 遺伝子シンボル (例: "TP53")
+        project_id: str — プロジェクト ID
+        consequence_type: str — 変異タイプ
+            (例: "missense_variant")
+        limit: int — 最大結果数
+    """
+    url = f"{ICGC_BASE}/mutations"
+    filters = {}
+
+    if gene_symbol:
+        filters["gene"] = {"symbol": {"is": [gene_symbol]}}
+    if project_id:
+        filters["donor"] = {"projectId": {"is": [project_id]}}
+    if consequence_type:
+        filters["mutation"] = {
+            "consequenceType": {"is": [consequence_type]}
+        }
+
+    import json
+    params = {
+        "size": limit,
+        "filters": json.dumps(filters) if filters else "{}",
+    }
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", []):
+        # 主要な consequence 取得
+        consequences = hit.get("consequences", [])
+        top_cons = consequences[0] if consequences else {}
+
+        results.append({
+            "mutation_id": hit.get("id", ""),
+            "chromosome": hit.get("chromosome", ""),
+            "start": hit.get("start"),
+            "end": hit.get("end"),
+            "mutation": hit.get("mutation", ""),
+            "type": hit.get("type", ""),
+            "gene_symbol": top_cons.get("geneSymbol", ""),
+            "consequence_type": top_cons.get("type", ""),
+            "aa_mutation": top_cons.get("aaMutation", ""),
+            "affected_donors": hit.get(
+                "affectedDonorCountTotal", 0),
+            "affected_projects": hit.get(
+                "affectedProjectCount", 0),
+            "functional_impact": hit.get(
+                "functionalImpact", ""),
+        })
+
+    df = pd.DataFrame(results)
+    if not df.empty:
+        df = df.sort_values("affected_donors",
+                            ascending=False)
+
+    total = data.get("pagination", {}).get("total", 0)
+    print(f"ICGC mutations: {len(df)}/{total} "
+          f"(gene={gene_symbol}, project={project_id})")
+    return df
+```
+
+## 3. がん種統計・変異サマリー
+
+```python
+def icgc_cancer_stats(project_id=None):
+    """
+    ICGC — がん種統計サマリー。
+
+    Parameters:
+        project_id: str — プロジェクト ID (None で全体統計)
+    """
+    if project_id:
+        url = f"{ICGC_BASE}/projects/{project_id}"
+        resp = requests.get(url, timeout=30)
+        resp.raise_for_status()
+        data = resp.json()
+
+        stats = {
+            "project_id": project_id,
+            "project_name": data.get("name", ""),
+            "primary_site": data.get("primarySite", ""),
+            "total_donors": data.get("totalDonorCount", 0),
+            "total_specimens": data.get(
+                "totalSpecimenCount", 0),
+            "ssm_count": data.get("ssmCount", 0),
+            "repository": "; ".join(
+                data.get("repository", [])),
+        }
+        print(f"ICGC stats: {project_id} — "
+              f"{stats['total_donors']} donors, "
+              f"{stats['ssm_count']} mutations")
+        return stats
+    else:
+        # 全プロジェクト概要
+        projects = icgc_search_projects(limit=200)
+        summary = {
+            "total_projects": len(projects),
+            "total_donors": projects[
+                "total_donors"].sum(),
+            "total_ssm": projects["ssm_count"].sum(),
+            "top_sites": projects.groupby(
+                "primary_site")["total_donors"].sum(
+                ).sort_values(ascending=False).head(10
+                ).to_dict(),
+        }
+        print(f"ICGC summary: {summary['total_projects']} "
+              f"projects, {summary['total_donors']} donors")
+        return summary
+
+
+def icgc_gene_mutation_frequency(gene_symbol, top_n=20):
+    """
+    ICGC — 遺伝子別がん種変異頻度。
+
+    Parameters:
+        gene_symbol: str — 遺伝子シンボル
+        top_n: int — 上位がん種数
+    """
+    mutations = icgc_search_mutations(
+        gene_symbol=gene_symbol, limit=500)
+
+    if mutations.empty:
+        return pd.DataFrame()
+
+    # プロジェクト別集計
+    freq = mutations.groupby("gene_symbol").agg(
+        total_mutations=("mutation_id", "count"),
+        total_affected_donors=("affected_donors", "sum"),
+        mutation_types=("consequence_type",
+                        lambda x: "; ".join(x.unique()[:5])),
+    ).reset_index()
+
+    print(f"ICGC gene frequency: {gene_symbol} — "
+          f"{len(freq)} entries")
+    return freq
+```
+
+## 4. ICGC 統合パイプライン
+
+```python
+def icgc_pipeline(gene_symbols, cancer_site=None,
+                     output_dir="results"):
+    """
+    ICGC 統合パイプライン。
+
+    Parameters:
+        gene_symbols: list[str] — 遺伝子リスト
+        cancer_site: str — がん部位フィルタ
+        output_dir: str — 出力ディレクトリ
+    """
+    from pathlib import Path
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # 1) プロジェクト検索
+    projects = icgc_search_projects(query=cancer_site)
+    projects.to_csv(output_dir / "projects.csv", index=False)
+
+    # 2) 遺伝子別変異検索
+    all_mutations = []
+    for gene in gene_symbols:
+        try:
+            muts = icgc_search_mutations(
+                gene_symbol=gene, limit=200)
+            muts["query_gene"] = gene
+            all_mutations.append(muts)
+        except Exception as e:
+            print(f"  Warning: {gene} — {e}")
+            continue
+
+    if all_mutations:
+        combined = pd.concat(all_mutations,
+                              ignore_index=True)
+        combined.to_csv(output_dir / "mutations.csv",
+                        index=False)
+
+    # 3) がん種統計
+    if not projects.empty:
+        top_project = projects.iloc[0]["project_id"]
+        stats = icgc_cancer_stats(project_id=top_project)
+        pd.DataFrame([stats]).to_csv(
+            output_dir / "cancer_stats.csv", index=False)
+
+    print(f"ICGC pipeline: {output_dir}")
+    return {"projects": projects}
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| (direct) | ICGC DCC API | 直接 REST API — TU 非連携 |
+
+## パイプライン統合
+
+```
+cancer-genomics → icgc-cancer-data → precision-oncology
+  (がんゲノム全般)  (ICGC DCC API)   (精密腫瘍学)
+       │                 │                 ↓
+  tcga-data ────────────┘        clinical-decision-support
+  (TCGA データ)      │            (臨床意思決定)
+                     ↓
+          variant-interpretation
+          (変異臨床解釈)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/projects.csv` | プロジェクト一覧 | → cancer-genomics |
+| `results/mutations.csv` | 体細胞変異 | → variant-interpretation |
+| `results/cancer_stats.csv` | がん種統計 | → precision-oncology |

package/src/.github/skills/scientific-pharmgkb-pgx/SKILL.md

@@ -0,0 +1,306 @@
+---
+name: scientific-pharmgkb-pgx
+description: |
+  PharmGKB 薬理ゲノミクススキル。PharmGKB REST API による
+  臨床アノテーション・薬物遺伝子関連・投与量ガイドライン・
+  スターアレル解析。ToolUniverse 連携: pharmgkb。
+tu_tools:
+  - key: pharmgkb
+    name: PharmGKB
+    description: 臨床アノテーション・薬物遺伝子関連・PGx ガイドライン
+---
+
+# Scientific PharmGKB PGx
+
+PharmGKB (Pharmacogenomics Knowledgebase) REST API を活用した
+薬理ゲノミクス臨床アノテーション・薬物遺伝子相互作用・投与量
+ガイドライン検索パイプラインを提供する。
+
+## When to Use
+
+- 薬物と遺伝子変異の関連を調べるとき
+- 臨床アノテーション (エビデンスレベル付き) を検索するとき
+- 投与量調整ガイドライン (CPIC/DPWG) を取得するとき
+- スターアレルと表現型の対応を確認するとき
+- 特定薬物の薬理ゲノミクス情報を包括的に取得するとき
+- 精密医療の薬物選択を支援するとき
+
+---
+
+## Quick Start
+
+## 1. 薬物・遺伝子検索
+
+```python
+import requests
+import pandas as pd
+
+PGKB_BASE = "https://api.pharmgkb.org/v1/data"
+
+
+def pharmgkb_search_drugs(query, limit=50):
+    """
+    PharmGKB — 薬物検索。
+
+    Parameters:
+        query: str — 薬物名 (例: "warfarin", "clopidogrel")
+        limit: int — 最大結果数
+    """
+    url = f"{PGKB_BASE}/chemical"
+    params = {"name": query, "view": "max"}
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for item in data.get("data", []):
+        results.append({
+            "pharmgkb_id": item.get("id", ""),
+            "name": item.get("name", ""),
+            "generic_names": "; ".join(
+                item.get("genericNames", [])),
+            "trade_names": "; ".join(
+                item.get("tradeNames", [])[:5]),
+            "type": item.get("type", ""),
+            "cross_references": len(
+                item.get("crossReferences", [])),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"PharmGKB drugs: {len(df)} results "
+          f"(query='{query}')")
+    return df
+
+
+def pharmgkb_search_genes(query, limit=50):
+    """
+    PharmGKB — 遺伝子検索。
+
+    Parameters:
+        query: str — 遺伝子シンボル (例: "CYP2D6")
+        limit: int — 最大結果数
+    """
+    url = f"{PGKB_BASE}/gene"
+    params = {"symbol": query, "view": "max"}
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for item in data.get("data", []):
+        results.append({
+            "pharmgkb_id": item.get("id", ""),
+            "symbol": item.get("symbol", ""),
+            "name": item.get("name", ""),
+            "chromosome": item.get("chromosomeFormatted", ""),
+            "cpic_gene": item.get("cpicGene", False),
+            "has_prescribing_info": item.get(
+                "hasPrescribingInfo", False),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"PharmGKB genes: {len(df)} results "
+          f"(query='{query}')")
+    return df
+```
+
+## 2. 臨床アノテーション取得
+
+```python
+def pharmgkb_clinical_annotations(gene_or_drug,
+                                     search_type="gene"):
+    """
+    PharmGKB — 臨床アノテーション検索。
+
+    Parameters:
+        gene_or_drug: str — 遺伝子シンボル or 薬物名
+        search_type: str — "gene" or "drug"
+    """
+    url = f"{PGKB_BASE}/clinicalAnnotation"
+    params = {"view": "max"}
+
+    if search_type == "gene":
+        # 遺伝子で検索
+        gene_url = f"{PGKB_BASE}/gene"
+        g_resp = requests.get(gene_url,
+                              params={"symbol": gene_or_drug},
+                              timeout=30)
+        g_resp.raise_for_status()
+        genes = g_resp.json().get("data", [])
+        if genes:
+            params["relatedGenes.id"] = genes[0].get("id", "")
+    else:
+        # 薬物で検索
+        drug_url = f"{PGKB_BASE}/chemical"
+        d_resp = requests.get(drug_url,
+                              params={"name": gene_or_drug},
+                              timeout=30)
+        d_resp.raise_for_status()
+        drugs = d_resp.json().get("data", [])
+        if drugs:
+            params["relatedChemicals.id"] = drugs[0].get("id", "")
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for item in data.get("data", []):
+        genes = [g.get("symbol", "")
+                 for g in item.get("relatedGenes", [])]
+        drugs = [c.get("name", "")
+                 for c in item.get("relatedChemicals", [])]
+        results.append({
+            "annotation_id": item.get("id", ""),
+            "level": item.get("level", ""),
+            "score": item.get("score", ""),
+            "genes": "; ".join(genes),
+            "drugs": "; ".join(drugs),
+            "phenotype_category": item.get(
+                "phenotypeCategory", ""),
+            "sentences": (item.get("textHtml") or "")[:300],
+        })
+
+    df = pd.DataFrame(results)
+    if not df.empty:
+        df = df.sort_values("level")
+
+    print(f"PharmGKB annotations: {len(df)} "
+          f"({search_type}={gene_or_drug})")
+    return df
+```
+
+## 3. 投与量ガイドライン取得
+
+```python
+def pharmgkb_dosing_guidelines(drug_name=None, gene=None):
+    """
+    PharmGKB — 投与量ガイドライン (CPIC/DPWG) 検索。
+
+    Parameters:
+        drug_name: str — 薬物名
+        gene: str — 遺伝子シンボル
+    """
+    url = f"{PGKB_BASE}/guideline"
+    params = {"view": "max"}
+
+    if drug_name:
+        params["relatedChemicals.name"] = drug_name
+    if gene:
+        params["relatedGenes.symbol"] = gene
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for item in data.get("data", []):
+        genes = [g.get("symbol", "")
+                 for g in item.get("relatedGenes", [])]
+        drugs = [c.get("name", "")
+                 for c in item.get("relatedChemicals", [])]
+        results.append({
+            "guideline_id": item.get("id", ""),
+            "name": item.get("name", ""),
+            "source": item.get("source", ""),
+            "genes": "; ".join(genes),
+            "drugs": "; ".join(drugs),
+            "recommendation": (item.get("textHtml") or "")[:500],
+        })
+
+    df = pd.DataFrame(results)
+    print(f"PharmGKB guidelines: {len(df)} "
+          f"(drug={drug_name}, gene={gene})")
+    return df
+```
+
+## 4. PharmGKB 統合パイプライン
+
+```python
+def pharmgkb_pipeline(drug_name, genes=None,
+                         output_dir="results"):
+    """
+    PharmGKB 統合パイプライン。
+
+    Parameters:
+        drug_name: str — 薬物名
+        genes: list[str] — 関連遺伝子リスト
+        output_dir: str — 出力ディレクトリ
+    """
+    from pathlib import Path
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # 1) 薬物検索
+    drugs = pharmgkb_search_drugs(drug_name)
+    drugs.to_csv(output_dir / "drugs.csv", index=False)
+
+    # 2) 薬物の臨床アノテーション
+    annotations = pharmgkb_clinical_annotations(
+        drug_name, search_type="drug")
+    annotations.to_csv(output_dir / "annotations.csv",
+                       index=False)
+
+    # 3) 投与量ガイドライン
+    guidelines = pharmgkb_dosing_guidelines(
+        drug_name=drug_name)
+    guidelines.to_csv(output_dir / "guidelines.csv",
+                      index=False)
+
+    # 4) 関連遺伝子解析
+    if genes:
+        gene_results = []
+        for g in genes:
+            try:
+                g_ann = pharmgkb_clinical_annotations(
+                    g, search_type="gene")
+                g_ann["query_gene"] = g
+                gene_results.append(g_ann)
+            except Exception:
+                continue
+        if gene_results:
+            gene_df = pd.concat(gene_results,
+                                ignore_index=True)
+            gene_df.to_csv(
+                output_dir / "gene_annotations.csv",
+                index=False)
+
+    print(f"PharmGKB pipeline: {output_dir}")
+    return {
+        "drugs": drugs,
+        "annotations": annotations,
+        "guidelines": guidelines,
+    }
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| `pharmgkb` | PharmGKB | 臨床アノテーション・薬物遺伝子・PGx ガイドライン |
+
+## パイプライン統合
+
+```
+pharmacogenomics → pharmgkb-pgx → clinical-decision-support
+  (PGx 解析全般)  (PharmGKB API)  (臨床意思決定)
+       │                │                ↓
+  drug-discovery ──────┘         precision-oncology
+  (薬物開発)         │            (精密腫瘍学)
+                     ↓
+           variant-interpretation
+           (変異臨床解釈)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/drugs.csv` | 薬物情報 | → drug-discovery |
+| `results/annotations.csv` | 臨床アノテーション | → variant-interpretation |
+| `results/guidelines.csv` | 投与量ガイドライン | → clinical-decision-support |
+| `results/gene_annotations.csv` | 遺伝子別アノテーション | → pharmacogenomics |